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- PDB-1r2m: Atomic resolution structure of the HFBII hydrophobin: a self-asse... -

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Basic information

Entry
Database: PDB / ID: 1r2m
TitleAtomic resolution structure of the HFBII hydrophobin: a self-assembling amphiphile
ComponentsHydrophobin II
Keywordssurface active protein / amphiphile / fungi / self-assembly / protein surfactant
Function / homology
Function and homology information


spore wall / extracellular region
Similarity search - Function
Cerato-ulmin hydrophobin family / Fungal hydrophobin / hfbii hydrophobin / Hydrophobin / Hydrophobin superfamily / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1 Å
AuthorsHakanpaa, J. / Paananen, A. / Askolin, S. / Nakari-Setala, T. / Parkkinen, T. / Penttila, M. / Linder, M.B. / Rouvinen, J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Atomic resolution structure of the HFBII hydrophobin, a self-assembling amphiphile.
Authors: Hakanpaa, J. / Paananen, A. / Askolin, S. / Nakari-Setala, T. / Parkkinen, T. / Penttila, M. / Linder, M.B. / Rouvinen, J.
History
DepositionSep 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hydrophobin II
B: Hydrophobin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4583
Polymers14,4032
Non-polymers551
Water4,522251
1
A: Hydrophobin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2562
Polymers7,2011
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hydrophobin II


Theoretical massNumber of molelcules
Total (without water)7,2011
Polymers7,2011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.657, 46.310, 34.593
Angle α, β, γ (deg.)90.00, 112.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1008-

HOH

21B-140-

HOH

31B-184-

HOH

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Components

#1: Protein Hydrophobin II / / HFBII


Mass: 7201.474 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Hypocrea jecorina (fungus) / Strain: QM9414 / References: UniProt: P79073
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 2000, LiSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
125 %PEG20001reservoir
20.2 Mlithium sulfate1reservoir
310 mM1reservoirMnCl2
40.1 Msodium HEPES1reservoirpH7.5
58 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.8126 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 17, 2002
RadiationMonochromator: triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8126 Å / Relative weight: 1
ReflectionResolution: 1→25 Å / Num. obs: 61978 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.45 % / Biso Wilson estimate: 9.2 Å2 / Rsym value: 0.063 / Net I/σ(I): 7.6
Reflection shellResolution: 1→1.02 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.235 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 25 Å / Num. measured all: 214050 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.235

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
ACORNphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1→25 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.975 / SU B: 0.254 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 0 / ESU R: 0.023 / ESU R Free: 0.023 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15316 3165 5.1 %RANDOM
Rwork0.13706 ---
obs0.13789 58818 99.77 %-
all-61978 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.916 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20.31 Å2
2---0.16 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1009 0 1 251 1261
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221028
X-RAY DIFFRACTIONr_bond_other_d0.0020.02951
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.9941403
X-RAY DIFFRACTIONr_angle_other_deg0.78932235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.615138
X-RAY DIFFRACTIONr_chiral_restr0.070.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021092
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02152
X-RAY DIFFRACTIONr_nbd_refined0.4450.2279
X-RAY DIFFRACTIONr_nbd_other0.2470.21140
X-RAY DIFFRACTIONr_nbtor_other0.0810.2561
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2149
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0940.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1990.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.251
X-RAY DIFFRACTIONr_mcbond_it0.7711.5720
X-RAY DIFFRACTIONr_mcangle_it1.24821157
X-RAY DIFFRACTIONr_scbond_it1.3093308
X-RAY DIFFRACTIONr_scangle_it2.0394.5246
X-RAY DIFFRACTIONr_rigid_bond_restr0.67421028
X-RAY DIFFRACTIONr_sphericity_free1.6972252
X-RAY DIFFRACTIONr_sphericity_bonded1.50621011
LS refinement shellResolution: 1→1.026 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.186 240
Rwork0.168 4333
Refinement
*PLUS
Highest resolution: 1 Å / Lowest resolution: 25 Å / Rfactor Rfree: 0.155 / Rfactor Rwork: 0.138
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.394
LS refinement shell
*PLUS
Rfactor Rfree: 0.188 / Rfactor Rwork: 0.172

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